A hierarchical model of non-homogeneous Poisson processes for Twitter retweets

We present a hierarchical model of nonhomogeneous Poisson processes (NHPP) for information diffusion on online social media, in particular Twitter retweets. The retweets of each original tweet are modelled by a NHPP, for which the intensity function is a product of time-decaying components and another component that depends on the follower count of the original tweet author. The latter allows us to explain or predict the ultimate retweet count by a network centrality-related covariate. The inference algorithm enables the Bayes factor to be computed, to facilitate model selection. Finally, the model is applied to the retweet datasets of two hashtags. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplemen

Retention versus sacrifice of the posterior cruciate ligament in total knee arthroplasty for treating osteoarthritis

Background The functional and clinical basis on which to choose whether or not to retain the posterior cruciate ligament during total knee arthroplasty surgery remained unclear after a Cochrane systematic review and meta-analysis in 2005, which contained eight clinical trials. Several new trials have been conducted since then. Hence, an update of the review was performed. Objectives Our aim was to assess the benefits and harms of retention compared to sacrifice of the posterior cruciate ligament in total knee arthroplasty in patients with osteoarthritis of the knee. Search methods An extensive search was conducted in CENTRAL, MEDLINE (PubMed), EMBASE, Web of Science, CINAHL, Academic Search Premier, Current Contents Connect and Science Direct. All databases were searched, without any limitations, up to 6 December 2012. References of the articles were checked and citation tracking was performed. Selection criteria Randomised and quasi-randomised controlled trials comparing retention with sacrifice of the posterior cruciate ligament in primary total knee arthroplasty in patients with osteoarthritis of the knee. Data collection and analysis Data were collected with a pre-developed form. Risk of bias was assessed independently by two authors (WV, LB). The level of evidence was graded using the GRADE approach. Meta-analysis was performed by pooling the results of the selected studies, when possible. Subgroup analyses were performed for posterior cruciate ligament retention versus sacrifice using the same total knee arthroplasty design, and for studies using a posterior cruciate ligament retaining or posterior stabilised design, and when sufficient studies were available subgroup analyses were performed for the same brand. Main results Seventeen randomised controlled trials (with 1810 patients and 2206 knees) were found, described in 18 articles. Ten of these were new studies compared to the previous Cochrane Review. One study from the original Cochrane review was excluded. Most new studies compared a posterior cruciate ligament retaining design with a posterior stabilised design, in which the posterior cruciate ligament is sacrificed (a posterior stabilised design has an insert with a central post which can engage on a femoral cam during flexion). The quality of evidence (graded with the GRADE approach) and the risk of bias were highly variable, ranging from moderate to low quality evidence and with unclear or low risk of bias for most domains, respectively. The performance outcome 'range of motion' was 2.4 degrees higher in favour of posterior cruciate ligament sacrifice (118.3 degrees versus 115.9 degrees; 95% confidence interval (CI) of the difference 0.13 to 4.67; P = 0.04), however the results were heterogeneous. On the item 'knee pain' as experienced by patients, meta-analysis could be performed on the Knee Society knee pain score; this score was 48.3 in both groups, yielding no difference between the groups. Implant survival rate could not be meta-analysed adequately since randomised controlled trials lack the longer term follow-up in order to evaluate implant survival. A total of four revisions in the cruciate-retention and four revisions in the cruciate-sacrifice group were found. The well-validated Western Ontario and McMaster Universities osteoarthritis index (WOMAC) total score was not statistically significantly different between the groups (16.6 points for cruciate-retention versus 15.0 points for cruciate-sacrifice). One study reported a patient satisfaction grade (7.7 points for cruciate-retention versus 7.9 points for cruciate-sacrifice on a scale from 0 to 10, 10 being completely satisfied) which did not differ statistically significantly. Complications were distributed equally between both groups. Only one study reported several re-operations other than revision surgery; that is patella luxations, surgical manipulation because of impaired flexion. The mean functional Knee Society Score was 2.3 points higher (81.2 versus 79.0 points; 95% CI of the difference 0.37 to 4.26; P = 0.02) in the posterior cruciate ligament sacrificing group. Results from the outcome Knee Society functional score were homogeneous. All other outcome measures (extension angle, knee pain, adverse effects, clinical questionnaire scores, Knee Society clinical scores, radiological rollback, radiolucencies, femorotibial angle and tibial slope) showed no statistically significant differences between the groups. In the subgroup analyses that allowed pooling of the results of the different studies, no homogeneous statistically significant differences were identified. Authors' conclusions The methodological quality and the quality of reporting of the studies were highly variable. With respect to range of motion, pain, clinical, and radiological outcomes, no clinically relevant differences were found between total knee arthroplasty with retention or sacrifice of the posterior cruciate ligament. Two statistically significant differences were found; range of motion was 2.4 degrees higher in the posterior cruciate ligament sacrificing group, however results were heterogeneous; and the mean functional Knee Society Score was 2.3 points higher in the posterior cruciate ligament sacrificing group. These differences are clinically not relevant

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes

Dynamic social networks in guppies (Poecilia reticulata)

One of the main challenges in the study of social networks in vertebrates is to close the gap between group patterns and dynamics. Usually scan samples or transect data are recorded to provide information about social patterns of animals, but these techniques themselves do not shed much light on the underlying dynamics of such groups. Here we show an approach which captures the fission-fusion dynamics of a fish population in the wild and demonstrates how the gap between pattern and dynamics may be closed. Our analysis revealed that guppies have complex association patterns that are characterised by close strong connections between individuals of similar behavioural type. Intriguingly, the preference for particular social partners is not expressed in the length of associations but in their frequency. Finally, we show that the observed association preferences could have important consequences for transmission processes in animal social networks, thus moving the emphasis of network research from descriptive mechanistic studies to functional and predictive ones. © 2014 Springer-Verlag Berlin Heidelberg

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls

Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix occidentalis caurina) in 11 study areas in Washington, Oregon, and northern California, USA. We estimated apparent survival, fecundity, recruitment, rate of population change, and local extinction and colonization rates, and investigated relationships between these parameters and the amount of suitable habitat, local and regional variation in meteorological conditions, and competition with Barred Owls (Strix varia). Data were analyzed for each area separately and in a meta-analysis of all areas combined, following a strict protocol for data collection, preparation, and analysis. We used mixed effects linear models for analyses of fecundity, Cormack-Jolly-Seber open population models for analyses of apparent annual survival (ϕ), and a reparameterization of the Jolly-Seber capture–recapture model (i.e. reverse Jolly-Seber; RJS) to estimate annual rates of population change (λ[subscript]RJS) and recruitment. We also modeled territory occupancy dynamics of Northern Spotted Owls and Barred Owls in each study area using 2-species occupancy models. Estimated mean annual rates of population change (λ) suggested that Spotted Owl populations declined from 1.2% to 8.4% per year depending on the study area. The weighted mean estimate of λ for all study areas was 0.962 (± 0.019 SE; 95% CI: 0.925–0.999), indicating an estimated range-wide decline of 3.8% per year from 1985 to 2013. Variation in recruitment rates across the range of the Spotted Owl was best explained by an interaction between total winter precipitation and mean minimum winter temperature. Thus, recruitment rates were highest when both total precipitation (29 cm) and minimum winter temperature (−9.5°C) were lowest. Barred Owl presence was associated with increased local extinction rates of Spotted Owl pairs for all 11 study areas. Habitat covariates were related to extinction rates for Spotted Owl pairs in 8 of 11 study areas, and a greater amount of suitable owl habitat was generally associated with decreased extinction rates. We observed negative effects of Barred Owl presence on colonization rates of Spotted Owl pairs in 5 of 11 study areas. The total amount of suitable Spotted Owl habitat was positively associated with colonization rates in 5 areas, and more habitat disturbance was associated with lower colonization rates in 2 areas. We observed strong declines in derived estimates of occupancy in all study areas. Mean fecundity of females was highest for adults (0.309 ± 0.027 SE), intermediate for 2-yr-olds (0.179 ± 0.040 SE), and lowest for 1-yr-olds (0.065 ± 0.022 SE). The presence of Barred Owls and habitat covariates explained little of the temporal variation in fecundity in most study areas. Climate covariates occurred in competitive fecundity models in 8 of 11 study areas, but support for these relationships was generally weak. The fecundity meta-analysis resulted in 6 competitive models, all of which included the additive effects of geographic region and annual time variation. The 2 top-ranked models also weakly supported the additive negative effects of the amount of suitable core area habitat, Barred Owl presence, and the amount of edge habitat on fecundity. We found strong support for a negative effect of Barred Owl presence on apparent survival of Spotted Owls in 10 of 11 study areas, but found few strong effects of habitat on survival at the study area scale. Climate covariates occurred in top or competitive survival models for 10 of 11 study areas, and in most cases the relationships were as predicted; however, there was little consistency among areas regarding the relative importance of specific climate covariates. In contrast, meta-analysis results suggested that Spotted Owl survival was higher across all study areas when the Pacific Decadal Oscillation (PDO) was in a warming phase and the Southern Oscillation Index (SOI) was negative, with a strongly negative SOI indicative of El Niño events. The best model that included the Barred Owl covariate (BO) was ranked 4th and also included the PDO covariate, but the BO effect was strongly negative. Our results indicated that Northern Spotted Owl populations were declining throughout the range of the subspecies and that annual rates of decline were accelerating in many areas. We observed strong evidence that Barred Owls negatively affected Spotted Owl populations, primarily by decreasing apparent survival and increasing local territory extinction rates. However, the amount of suitable owl habitat, local weather, and regional climatic patterns also were related to survival, occupancy (via colonization rate), recruitment, and, to a lesser extent, fecundity, although there was inconsistency in regard to which covariates were important for particular demographic parameters or across study areas. In the study areas where habitat was an important source of variation for Spotted Owl demographics, vital rates were generally positively associated with a greater amount of suitable owl habitat. However, Barred Owl densities may now be high enough across the range of the Northern Spotted Owl that, despite the continued management and conservation of suitable owl habitat on federal lands, the long-term prognosis for the persistence of Northern Spotted Owls may be in question without additional management intervention. Based on our study, the removal of Barred Owls from the Green Diamond Resources (GDR) study area had rapid, positive effects on Northern Spotted Owl survival and the rate of population change, supporting the hypothesis that, along with habitat conservation and management, Barred Owl removal may be able to slow or reverse Northern Spotted Owl population declines on at least a localized scale.Keywords: Northern Spotted Owl, occupancy, population change, Strix varia, Strix occidentalis caurina, fecundity, Barred Owl, surviva

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist